TLR9 is an endosomally localized Pattern Recognition Receptor (PRR) that detects pathogen-associated DNA. TLR9 traffics from in the Endoplasmic Reticulum (ER) to the endolysosome, where it is cleaved and made competent for signaling activation. We have recently demonstrated that TLR9 is ubiquitinated and targeting of TLR9 to the early endosome is an ubiquitin-dependent process that is mediated by the ESCRT protein Hepatocyte Growth Factor Regulated Tyrosine Kinase Substrate (HRS). This compartmentalization is critical in mediating the signaling activation, as well as reducing the likelihood of triggering autoimmune disease. However, the molecular cofactors that enable TLR9 to transit from the ER to the endolysome are mostly uncharacterized. Here, we propose to identify the E3 ubiquitin ligase that is required for TLR9 ubiquitination using a high throughput genetic approach, as well as characterize the non-canonical role of ESCRT pathways components in TLR9 trafficking. In addition, we propose to validate 15 proteins identified by a genome-wide RNAi screen for TLR7/9 signaling for their potential roles in TLR7/9 endosomal trafficking. Finally, we propose to study the in vivo role of TLR9 ubiquitination and ESCRT function in TLR9 expressing cell subsets. Understanding the trafficking system of TLR9 is critical for the development of drugs for autoimmune diseases that results from promiscuous activation through endosomal TLR signaling.